MEXT Second Screening - Urgent Help!

Hi, I just recently passed the first screening but due to complications we had only less than 2 weeks between the announcement and the deadline for requesting Letters of Acceptance.

I am confused, do I need to apply to the universities too in this stage or is it completely settled by MEXT? Some of the universities have not even opened yet the registration for the Fall 2021 intake, and if they were it would be far from the request deadline. One of the universities on the other hand opened their registration in this week only!

Any clarification would be greatly appreciated!